[ccp4bb] extra high B factor - Summary

2007-05-01 Thread Jiamu Du
Dear All: Thank you for help. Now I will make a summary of this topic. First, the actual situation is that: 1. Protein and peptide have a affinity about 10E-7 to 10E-8 molar. 2. The 2.6 angstrom data were got from a co-crystal and had a wilson B about 70, in the experiment protein/peptide have a

Re: [ccp4bb] extra high B factor

2007-05-01 Thread Jiamu Du
age d'origine- > > *De :* CCP4 bulletin board [mailto: > CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > > <mailto:CCP4BB@JISCMAIL.AC.UK>>]*De la part de* Jiamu Du > > *Envoyé :* lundi 30 avril 2007 05:57 >

Re: [ccp4bb] extra high B factor

2007-04-30 Thread Bernhard Rupp
> If you assume atomic B-factors of 100 or larger and > calculate the density, I really can't see how this is possible. Well, I do. The recipe has been published in NSB as a cautionary tale. http://www.ruppweb.org/cvs/br/rupp_2001_NSB_questions_BotA.pdf and there is quite fail-safe away to inves

[ccp4bb] AW: [ccp4bb] extra high B factor

2007-04-30 Thread Herman . Schreuder
: Montag, 30. April 2007 16:32 An: CCP4BB@JISCMAIL.AC.UK Betreff: Re: [ccp4bb] extra high B factor Dear all, Frankly speaking I am having some doubts about this whole discussion. 1. Apparently, it does not make a difference in R and Rfree whether the peptide is in the structure or not. This does

Re: [ccp4bb] extra high B factor

2007-04-30 Thread mesters
mailto:CCP4BB@JISCMAIL.AC.UK>>]*De la part de* Jiamu Du > *Envoyé :* lundi 30 avril 2007 05:57 > *À :* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> <mailto:CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK>> > *Objet :* [c

Re: [ccp4bb] extra high B factor

2007-04-30 Thread Manfred S. Weiss
will be the value that you will > > > obtain after refinement... > > > > > > > > > Philippe Dumas > > > IBMC-CNRS, UPR9002 > > > 15, rue Ren? Descartes 67084 Strasbourg cedex > > > tel: +33 (0)3 88 41 70 02 > >

Re: [ccp4bb] extra high B factor

2007-04-30 Thread artis
will be the value that you will >> > obtain after refinement... >> > >> > >> > Philippe Dumas >> > IBMC-CNRS, UPR9002 >> > 15, rue René Descartes 67084 Strasbourg cedex >> > tel: +33 (0)3 88 41 70 02 >> >

Re: [ccp4bb] extra high B factor

2007-04-30 Thread Jiamu Du
K>]*De la part de* Jiamu Du > *Envoyé :* lundi 30 avril 2007 05:57 > *À :* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> > *Objet :* [ccp4bb] extra high B factor > > Dear All: > I am refining a protein-peptide complex struture at 2.6

Re: [ccp4bb] extra high B factor

2007-04-30 Thread Eleanor Dodson
*Envoyé :* lundi 30 avril 2007 05:57 *À :* CCP4BB@JISCMAIL.AC.UK <mailto:CCP4BB@JISCMAIL.AC.UK> *Objet :* [ccp4bb] extra high B factor Dear All: I am refining a protein-peptide complex struture at 2.6 angstrom resolution. The data wa

Re: [ccp4bb] extra high B factor

2007-04-30 Thread Jiamu Du
g cedex tel: +33 (0)3 88 41 70 02 [EMAIL PROTECTED] -Message d'origine- *De :* CCP4 bulletin board [mailto: [EMAIL PROTECTED] la part de*Jiamu Du *Envoyé :* lundi 30 avril 2007 05:57 *À :* CCP4BB@JISCMAIL.AC.UK *Objet :* [ccp4bb] extra high B factor Dear All: I am refining a protein

Re: [ccp4bb] extra high B factor

2007-04-29 Thread Juergen Bosch
Hi Jiamu, is the high B-value of your protein due to motions, which are not modeled appropiately ? Which program by the way are you using for refinement ? Then the TLSMD server might help you here. Monomer or multimer in the asu ? NCS used, if so checked that they actually follow NCS and you'

Re: [ccp4bb] extra high B factor

2007-04-29 Thread Jiamu Du
I will try it soon. If it work, I will paste a sumary. Thanks On 4/30/07, Jacqueline Vitali <[EMAIL PROTECTED]> wrote: Hello, I think it is because the peptide does not have full occupancy. I do not know if it is OK to fix occupancy to 0.5 and do the refinement. That would bring temp factor

[ccp4bb] extra high B factor

2007-04-29 Thread Jiamu Du
Dear All: I am refining a protein-peptide complex struture at 2.6 angstrom resolution. The data was obtain from a co-crystal and the wilson B factor of the data is about 70. The affinity between protein and peptide is about 10E-7 to 10E-8 molar. Protein fragment of the structure has a common B fac